Andrew Burrell – They may not like being lumped together, but Indonesia's radical Islamic terrorists and the nation's military commanders have more in common than they would care to admit.

Most glaringly, they are both accused of using or authorising shocking violence, often leading to the death of many innocent civilians, in the pursuit of their goals.

For the terrorists, that goal is apparently the eradication of Western influences from Indonesia, and even the establishment of a pan-Islamic state. The military's raison d'etre, according to current thinking, is to preserve the unitary state of Indonesia at any cost.

Indonesia's Muslim radicals and the most brutal of its military men have done more than just about any other group to damage Indonesia's international reputation in recent years.

The Bali bombings last October and the military-backed bloodshed in East Timor in 1999 horrified the world, created a general climate of insecurity in Indonesia and scared away foreign investment.

The killings last year of two American school teachers in Papua, a crime which is strongly believed to be linked to the military (TNI) but predictably remains unsolved, is causing a rift with Washington.

Indonesia is therefore sending a profound message to the world that it will deal with the alleged crimes committed by these two groups in very different ways.

The rule seems to be: Muslim militants who kill people will be chased to the four corners of the globe and then sentenced to death, but TNI troops accused of the same crimes should feel relatively safe.

This hypocrisy has been highlighted in the past two days. On Monday, Indonesia basked again in its new found reputation for cracking down on home-grown terrorists, revealing that a key suspect in last year's Bali bombings had been nabbed while planning another attack. The arrest of Idris, a suspected Jemaah Islamiyah member who allegedly organised the financing of the Bali operation and had been on the run for the past nine months, is certainly significant as it could help police and prosecutors shed more light on the terrorists' money trail across South-East Asia.

Indonesia has taken the world by surprise by arresting, with the help of the Australian Federal Police, more than 30 of the militants believed to have planned and carried out the Bali bombings.

Prosecutors on Monday also formally called for the death penalty for the first of the alleged bombers to face trial, a Javanese mechanic called Amrozi whom defence lawyers have attempted to distance from the crime in an attempt to spare him the firing squad.

Within the next few weeks, Amrozi will be become the first alleged Bali bomber to be told of his fate, although he will have the option of an appeal which could, in theory, extend his life by several months at least.

Amrozi's cohorts such as Imam Samudra, Ali Imron and Mukhlas are also facing death sentences under new legislation enacted by Indonesia after the bombings.

Of course, the Indonesian government does not regard human rights abuses by its military officers – even in the most visible areas of excess such as Aceh, Papua and East Timor – with anywhere near such seriousness.

In Jakarta yesterday, lawyers for the most senior military officer to be charged over the bloodshed in East Timor in 1999, Major-General Adam Damiri, were appearing before a panel of five judges to argue for his acquittal.

Damiri headed the regional military command overseeing East Timor and is the last of 18 defendants summoned to appear before the court over alleged human rights abuses committed against East Timorese independence supporters.

But the lawyers' submission appears to have been a mere formality as state prosecutors had already urged the court to acquit him.

After 15 months of running the case, the prosecution last month came to the conclusion that there was insufficient evidence to continue against Damiri, who is now a senior commander in Indonesia's war against separatists in Aceh.

It looked to be a decision made hastily, and, although there is no proof, it may have been a by-product of the current patriotic fervour in Jakarta, where surging nationalism has elevated to hero status the soldiers fighting to preserve the Indonesian state.

Regardless of the reasons for the prosecution's actions, the human rights court established by Jakarta under considerable international pressure is already considered a sham because most officers have walked free and none of the few found guilty have received hefty sentences.

Damiri, as the last and most senior officer to face trial over East Timor, appears destined to become a lasting symbol of the court's ineptitude, as well as the double standards of the wider justice system.